Alignments for a candidate for ilvI in Desulfovibrio vulgaris Miyazaki F

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Desulfovibrio vulgaris Miyazaki F

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate 8499376 DvMF_0153 acetolactate synthase, large subunit, biosynthetic type (RefSeq)

Query= metacyc::MONOMER-18810
         (585 letters)



>FitnessBrowser__Miya:8499376
          Length = 562

 Score =  605 bits (1559), Expect = e-177
 Identities = 313/565 (55%), Positives = 402/565 (71%), Gaps = 7/565 (1%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77
           E+ GA IL+  L  EGV+ ++GYPGGAV+ IYDEL +     HILVRHEQAAVHAADG+A
Sbjct: 2   ELNGARILLECLKREGVDVLFGYPGGAVIDIYDELPRHD-IRHILVRHEQAAVHAADGFA 60

Query: 78  RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137
           RA+GKVGV LVTSGPG TN VTGIATAY DSIPMVV+TG VPT  IG DAFQE D VGIT
Sbjct: 61  RASGKVGVCLVTSGPGATNTVTGIATAYADSIPMVVLTGQVPTPLIGNDAFQEVDIVGIT 120

Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197
           RP  KHN+LVKDVRDLA  +++AF++A +GRPGPV+VD+PKDV +   ++ +P+ + +RS
Sbjct: 121 RPCTKHNYLVKDVRDLARVLRQAFYLARSGRPGPVLVDLPKDVMQAKTEFVWPEDVKLRS 180

Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGL 257
           YNP  + +  Q+R+AV  L  A+RP  + GGGV++++AS+EL  LA     PVT+TLMGL
Sbjct: 181 YNPTYRPNLNQLRRAVEALIEAKRPLFFAGGGVIMSDASEELGWLARTLSIPVTSTLMGL 240

Query: 258 GAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHI 317
           GAFPG    ++GM+GMHGTY  N A+ N D ++A+GARFDDRV G  + F S AR IIHI
Sbjct: 241 GAFPGDDPLWLGMIGMHGTYAGNKAVNNADCIVAVGARFDDRVTGRLSAFASGAR-IIHI 299

Query: 318 DIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALA--KWWEQIEQWRSVD 375
           DIDP+SI K V+VDIP+VG+ +  L   I +I  + +  K  A A   W  Q+  WR+  
Sbjct: 300 DIDPTSIRKNVQVDIPVVGDCRKALAG-IREIATTRLAEKDWATAHEPWLTQVSAWRTEQ 358

Query: 376 CLKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLG 435
            L Y ++   IKPQ VVE I+ +T+GDA + ++VGQ+QMW AQF+ F +PR  + SGGLG
Sbjct: 359 PLTYVKNGS-IKPQQVVETIFSITRGDAIVTTEVGQNQMWTAQFFTFRKPRTLLTSGGLG 417

Query: 436 TMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMV 495
           TMG G P A+G + AFP+K V+ + G+GSIQM IQEL+T +    P+KI  LNNGYLGMV
Sbjct: 418 TMGYGFPAAIGAQFAFPDKLVIDMAGDGSIQMNIQELATAVCNKLPIKIVILNNGYLGMV 477

Query: 496 RQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFL 555
           RQWQE+ Y   Y  + M+A PDFVKLAEAYG  G R+ +  ++E  LR AF     T  +
Sbjct: 478 RQWQELFYQRNYCSTCMEAQPDFVKLAEAYGAEGYRITEAGELESTLRAAF-ASPHTAVI 536

Query: 556 DFQTDPTENVWPMVQAGKGISEMLL 580
           D + +  ENV+PMV AG  + EMLL
Sbjct: 537 DVRVEREENVYPMVPAGAALDEMLL 561


Lambda     K      H
   0.319    0.135    0.407 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 866
Number of extensions: 33
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 585
Length of database: 562
Length adjustment: 36
Effective length of query: 549
Effective length of database: 526
Effective search space:   288774
Effective search space used:   288774
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)

Align candidate 8499376 DvMF_0153 (acetolactate synthase, large subunit, biosynthetic type (RefSeq))
to HMM TIGR00118 (ilvB: acetolactate synthase, large subunit, biosynthetic type (EC 2.2.1.6))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR00118.hmm
# target sequence database:        /tmp/gapView.5617.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00118  [M=557]
Accession:   TIGR00118
Description: acolac_lg: acetolactate synthase, large subunit, biosynthetic type
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   3.1e-256  837.1   0.0   3.6e-256  836.9   0.0    1.0  1  lcl|FitnessBrowser__Miya:8499376  DvMF_0153 acetolactate synthase,


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8499376  DvMF_0153 acetolactate synthase, large subunit, biosynthetic type (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  836.9   0.0  3.6e-256  3.6e-256       1     554 [.       3     560 ..       3     562 .] 0.97

  Alignments for each domain:
  == domain 1  score: 836.9 bits;  conditional E-value: 3.6e-256
                         TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvlatsGPGatn 77 
                                       l+ga+il+e lk+egv+++fGyPGGav++iyd+l   +++hilvrheqaa+haadG+arasGkvGv+l+tsGPGatn
  lcl|FitnessBrowser__Miya:8499376   3 LNGARILLECLKREGVDVLFGYPGGAVIDIYDELPRHDIRHILVRHEQAAVHAADGFARASGKVGVCLVTSGPGATN 79 
                                       579************************************************************************** PP

                         TIGR00118  78 lvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeiastGrPGPvl 154
                                       +vtgiatay+ds+P+vvltGqv+t liG+dafqe+di+Git+p+tkh++lvk+++dl+++l++af++a +GrPGPvl
  lcl|FitnessBrowser__Miya:8499376  80 TVTGIATAYADSIPMVVLTGQVPTPLIGNDAFQEVDIVGITRPCTKHNYLVKDVRDLARVLRQAFYLARSGRPGPVL 156
                                       ***************************************************************************** PP

                         TIGR00118 155 vdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaeaseelkelaerlkipv 231
                                       vdlPkdv++a++e+  +e+v+l++y+pt +++ +q+++a+e++ +ak+P+ ++GgGvi+++aseel  la +l ipv
  lcl|FitnessBrowser__Miya:8499376 157 VDLPKDVMQAKTEFVWPEDVKLRSYNPTYRPNLNQLRRAVEALIEAKRPLFFAGGGVIMSDASEELGWLARTLSIPV 233
                                       ***************************************************************************** PP

                         TIGR00118 232 tttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapeakiihididPaeigknv 308
                                       t+tl+GlGafp d+pl lgm+GmhGt++ n av++ad+++avGarfddrvtg l+ fa+ a+iihididP++i knv
  lcl|FitnessBrowser__Miya:8499376 234 TSTLMGLGAFPGDDPLWLGMIGMHGTYAGNKAVNNADCIVAVGARFDDRVTGRLSAFASGARIIHIDIDPTSIRKNV 310
                                       ***************************************************************************** PP

                         TIGR00118 309 kvdipivGdakkvleellkklkee......ekkeke.WlekieewkkeyilkldeeeesikPqkvikelskllkdea 378
                                       +vdip+vGd++k l+ + + ++++        + +e Wl +++ w++e++l++  +++sikPq+v++++  +++++a
  lcl|FitnessBrowser__Miya:8499376 311 QVDIPVVGDCRKALAGIREIATTRlaekdwA-TAHEpWLTQVSAWRTEQPLTY-VKNGSIKPQQVVETIFSITRGDA 385
                                       **************98876655544444533.33346*************876.56799****************** PP

                         TIGR00118 379 ivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydi 455
                                       ivtt+vGq+qmw+aqf++++kpr+ +tsgGlGtmG+G+Paa+Ga+ a p++ v++++Gdgs+qmn+qel+t+v  ++
  lcl|FitnessBrowser__Miya:8499376 386 IVTTEVGQNQMWTAQFFTFRKPRTLLTSGGLGTMGYGFPAAIGAQFAFPDKLVIDMAGDGSIQMNIQELATAVCNKL 462
                                       ***************************************************************************** PP

                         TIGR00118 456 pvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldv 532
                                       p+kivilnn +lGmv+qWqelfy++ y +t++++ +pdfvklaeayG++g ri++  ele+ l+ a++s + +++dv
  lcl|FitnessBrowser__Miya:8499376 463 PIKIVILNNGYLGMVRQWQELFYQRNYCSTCMEA-QPDFVKLAEAYGAEGYRITEAGELESTLRAAFASPHTAVIDV 538
                                       *********************************5.****************************************** PP

                         TIGR00118 533 evdkeeevlPmvapGagldelv 554
                                       +v++ee+v+Pmv+ Ga+lde++
  lcl|FitnessBrowser__Miya:8499376 539 RVEREENVYPMVPAGAALDEML 560
                                       *********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (562 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 7.90
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for Amino acid biosynthesis